The 48-year-old was sent to the stands after Sime Vrsaljko’s early red card. He served the first match of his suspension as Atletico completed a 2-1 aggregate win on Thursday.
It is not the first time that the Argentine, who was also fined 10,000 euros (£8,800), has been in trouble.
In 2014, he was banned by the Spanish Football Federation for eight matches for his behaviour in the second leg of the Spanish Super Cup.
He got a four-game punishment for tapping the fourth official on the back of the head after a heated exchange during Atletico’s 2-1 aggregate win over Real Madrid, and a further sanction for protesting, applauding a red card and not leaving the field.
In 2016, he was given a touchline ban for the final three La Liga games of the season after appearing to instruct a ball boy to throw a ball on to the pitch to disrupt a Malaga attack during an Atletico victory.
Uefa’s control, ethics and disciplinary board also fined the club 10,000 euros after fans threw objects on the pitch at Emirates Stadium.